We used Single Strand Conformation Polymorphism (SSCP) of mtDNA control region to assess the population structure of the flatfish Pleuronectes platessa (plaice), to compare these data with a previous study based on microsatellite loci, and to test for possible sex-biased dispersal. From 461 individuals, 163 haplotypes were identified across 11 locations. Diversity was higher with mtDNA (h =0.776 to 0.981; π= 0.0178 to 0.0298) as compared to microsatellite loci using the same samples (He = 0.721 to 0.77). Genetic diversity was lower in samples from Iceland and Faroe, as compared to the continental shelf samples. Although both classes of markers revealed a relatively strong differentiation between shelf and off-shelf populations (q = 0.1015 and q = 0.0351, respectively), only the mtDNA data were able to detect differentiation within the continental shelf, i.e., a North Sea-Irish Sea group which was weakly distinguishable from Norway (q = 0.0046), the Baltic (q = 0.0136) and the Bay of Biscay (q = 0.0162). No evidence was obtained for isolation by distance, nor for sex-biased dispersal. This study demonstrates the importance of using more than one class of markers, especially for species such as plaice, with large populations, high dispersal and recent colonisation histories.